Soak beans in enough cold water to cover them by 2 inches for 6 hours or overnight. (Alternatively, use the quick-soak method: Place beans in a large pot with enough water to cover by 2 inches. Bring to a boil over high heat. Remove from heat and let stand for 1 hour.)
Drain the beans and place them in a slow cooker. Add onion, garlic, thyme and bay leaf. Pour in boiling water. Cook, covered, on high until beans are tender, 2 to 3 1/2 hours. Add salt, cover, and cook for 15 minutes more.